Should have mentioned that before...sorry. Windows. When I need to explore infected drives I sometimes boot to linux live cds/partitions but, in some cases that isn't a very good option. A linux distro that was geared towards virus detection and removal in windows filesystems would be awesome but I'm yet to run into one.
This thread got me thinking about the subject in a new way and, after some searching, I found this:
Trinity Rescue Kit | CPR for your computer
Seems pretty useful. I'm going to check it out. Still open to other ideas though! Maybe a hardware solution...?